Paolo Calligari
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View article: GROMODEX: Optimisation of GROMACS Performance through a Design of Experiment Approach
GROMODEX: Optimisation of GROMACS Performance through a Design of Experiment Approach Open
We introduce GROMODEX, a novel tool designed to optimise GROMACS molecular dynamics (MD) simulations using a structured Design of Experiments (DoE) approach. GROMACS, though efficient, requires extensive tuning of parameters to perform opt…
View article: Investigation of the Mechanism of Action of Natural and Synthetic Monoterpenoids: For a New Route in Antimycotic Molecules
Investigation of the Mechanism of Action of Natural and Synthetic Monoterpenoids: For a New Route in Antimycotic Molecules Open
Monoterpenoids are well‐recognized natural antimycotic agents, but their mechanism of action is still unclear. Interestingly, synthetic derivatives, such as 4‐bromothymol (4‐bromo‐2‐isopropyl‐5‐methylphenol), are emerging as promising alte…
View article: Mechanistic Insights into the Membrane Permeabilization Activity of Antimicrobial Prenylated Isoflavonoids: A Comparative Study of Glabridin, Wighteone, and Lupiwighteone
Mechanistic Insights into the Membrane Permeabilization Activity of Antimicrobial Prenylated Isoflavonoids: A Comparative Study of Glabridin, Wighteone, and Lupiwighteone Open
Prenylated isoflavonoids have shown remarkable antimicrobial activity. Previous studies showed that the antimicrobial compounds glabridin and wighteone induced membrane permeabilization in microbial cells. Other compounds, such as lupiwigh…
View article: Dominantly acting variants in ATP6V1C1 and ATP6V1B2 cause a multisystem phenotypic spectrum by altering lysosomal and/or autophagosome function
Dominantly acting variants in ATP6V1C1 and ATP6V1B2 cause a multisystem phenotypic spectrum by altering lysosomal and/or autophagosome function Open
The vacuolar H+-ATPase (V-ATPase) is a functionally conserved multimeric complex localized at the membranes of many organelles where its proton-pumping action is required for proper lumen acidification. The V-ATPase complex is c…
View article: Molecular and cellular evidence of a direct interaction between the TRAF2 C-terminal domain and ganglioside GM1
Molecular and cellular evidence of a direct interaction between the TRAF2 C-terminal domain and ganglioside GM1 Open
TNF receptor-associated factor 2 (TRAF2) is involved in different cellular processes including signal transduction and transcription regulation. We here provide evidence of a direct interaction between the TRAF domain of TRAF2 and the mono…
View article: Isoamphipathic antibacterial molecules regulating activity and toxicity through positional isomerism
Isoamphipathic antibacterial molecules regulating activity and toxicity through positional isomerism Open
Peptidomimetic antimicrobials exhibit a selective interaction with bacterial cells over mammalian cells once they have achieved an optimum amphiphilic balance (hydrophobicity/hydrophilicity) in the molecular architecture.
View article: Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein–Protein Interactions
Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting Its Protein–Protein Interactions Open
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in cell signaling and represents a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibit…
View article: Discriminating between competing models for the allosteric regulation of oncogenic phosphatase SHP2 by characterizing its active state
Discriminating between competing models for the allosteric regulation of oncogenic phosphatase SHP2 by characterizing its active state Open
View article: A Recurrent Gain-of-Function Mutation in CLCN6, Encoding the ClC-6 Cl−/H+-Exchanger, Causes Early-Onset Neurodegeneration
A Recurrent Gain-of-Function Mutation in CLCN6, Encoding the ClC-6 Cl−/H+-Exchanger, Causes Early-Onset Neurodegeneration Open
View article: Role of proteolytic enzymes in the COVID-19 infection and promising therapeutic approaches
Role of proteolytic enzymes in the COVID-19 infection and promising therapeutic approaches Open
View article: Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting its Protein-Protein Interactions
Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting its Protein-Protein Interactions Open
We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in multiple signaling pathways and a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhib…
View article: Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase
Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase Open
SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by PTPN11, plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations in PTPN11 are associated with different rare dis…
View article: Molecular Investigation of SARS–CoV-2 Proteins and Their Interactions with Antiviral Drugs
Molecular Investigation of SARS–CoV-2 Proteins and Their Interactions with Antiviral Drugs Open
A new Coronavirus strain, named SARS-CoV-2, suddenly emerged in early December 2019. SARS-CoV-2 resulted in being dramatically infectious, with thousands of people infected. In this scenario, and without effective vaccines available, the i…
View article: Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase
Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase Open
SH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded by PTPN11 , plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations in PTPN11 are associated with different rare diseases and hem…
View article: Nano-bio interactions: a neutrophil-centric view
Nano-bio interactions: a neutrophil-centric view Open
View article: Targeting the Pentose Phosphate Pathway: Characterization of a New 6PGL Inhibitor
Targeting the Pentose Phosphate Pathway: Characterization of a New 6PGL Inhibitor Open
View article: Mutations in KCNK4 that Affect Gating Cause a Recognizable Neurodevelopmental Syndrome
Mutations in KCNK4 that Affect Gating Cause a Recognizable Neurodevelopmental Syndrome Open
View article: Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors
Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors Open
View article: Integrated Computational Approach to the Electron Paramagnetic Resonance Characterization of Rigid 3<sub>10</sub>-Helical Peptides with TOAC Nitroxide Spin Labels
Integrated Computational Approach to the Electron Paramagnetic Resonance Characterization of Rigid 3<sub>10</sub>-Helical Peptides with TOAC Nitroxide Spin Labels Open
We address the interpretation, via an integrated computational approach, of the experimental continuous-wave electron paramagnetic resonance (cw-EPR) spectra of a complete set of conformationally highly restricted, stable 310-he…
View article: Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions
Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions Open
In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained descrip…